I think Anna was very annoyed at her character's treatment in the film. Didn't she say somewhere that she didn't agree with them curing Rogue? Can't remember...

I haven't heard of that. Though when asked what did her character do (in an informal interview with the other actresses) she said "I've got some gloves." and when asked about changed haircuts from X2 to X3, "I don't change, I never change, always the same". One more quote was "I've been in 3 action movies and never had any action. It's kind of amazing".
Halle complained a little too, and the whole interview was handled in a funny way...

Her answers were pretty controversial at the time. In a magazine interview, she says she's done with the X-movies. In Cannes, when asked if she would make an X4, she said "Absolutely." (it's in a video on Youtube) in a positive way. Now that quote from Reallycoolguy, which actually sounds positive to me. She also was the last to sign for X3.

I think only time will tell. To me, it will all depend on the creative team. If Ratner and the writers come back, I'm about sure she'll jump out. Unless everyone comes back and she gets an awesome role on the script.